0.015314
0.000000
0.000000
0.000000
0.010893
0.000000
0.000000
0.000000
0.014728
0.00000
0.00000
0.00000
Wang, L.K.
Lima, C.D.
Shuman, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
65.300
91.800
67.900
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
O4 S -2
96.063
SULFATE ION
non-polymer
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
N
296
N
O
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
S
N
305
N
O
N
306
N
O
N
307
N
O
N
308
N
O
N
309
N
N
N
310
S
C
N
311
N
C
N
312
N
O
N
313
R
C
N
314
N
O
N
315
N
C
N
316
N
O
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
N
N
327
S
C
N
328
N
C
N
329
N
O
N
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
N
Y
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
N
340
N
O
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
N
N
354
S
C
N
355
N
C
N
356
N
O
N
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
N
364
N
O
N
365
N
O
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
N
N
378
S
C
N
379
N
C
N
380
N
O
N
381
N
C
N
382
N
C
N
383
N
C
N
384
N
O
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
doub
N
291
N
doub
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
doub
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
doub
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
doub
Y
326
N
sing
Y
327
N
sing
N
328
N
sing
Y
329
N
sing
Y
330
N
doub
N
331
N
sing
Y
332
N
doub
N
333
N
sing
Y
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
doub
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
Y
349
N
doub
Y
350
N
sing
Y
351
N
sing
N
352
N
sing
Y
353
N
doub
N
354
N
sing
Y
355
N
doub
N
356
N
sing
Y
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
doub
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
UK
EMBO J.
EMJODG
0897
0261-4189
21
3873
3880
10.1093/emboj/cdf397
12110598
Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme.
2002
10.2210/pdb1ly1/pdb
pdb_00001ly1
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2001-11-15
MARRESEARCH
Si
SINGLE WAVELENGTH
M
x-ray
1
0.9790
1.0
X9A
NSLS
0.9790
SYNCHROTRON
NSLS BEAMLINE X9A
20670.787
polynucleotide kinase
2.7.1.78
kinase domain, residues 1-181
1
man
polymer
96.063
SULFATE ION
4
syn
non-polymer
18.015
water
142
nat
water
PNK, Polynucleotide 5'-hydroxyl-kinase
no
no
MKKIILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSIMAHEERDEYKYTKKKEGIVTGMQFDTAKSILYGGDSVKG
VIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWTELVKRNSKRGTKAVPIDVLRSMYKSMREYLGLPVYNGTPGKPK
AVIFDVDGTLAKMNGRGPYDL
MKKIILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSIMAHEERDEYKYTKKKEGIVTGMQFDTAKSILYGGDSVKG
VIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWTELVKRNSKRGTKAVPIDVLRSMYKSMREYLGLPVYNGTPGKPK
AVIFDVDGTLAKMNGRGPYDL
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
T4-like viruses
Enterobacteria phage T4 sensu lato
Escherichia
Escherichia coli
sample
PSET
10665
Enterobacteria phage T4
469008
Escherichia coli BL21(DE3)
BL21 DE3
PLASMID
PET
1
2.46
50.01
VAPOR DIFFUSION, HANGING DROP
4.6
0.1M NaOAc 4.6, 5mM DTT, 16% PEG2000MME, 0.4M AMSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-07-17
1
1
2008-04-28
1
2
2011-07-13
1
3
2024-02-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
HETEROGEN
The sulfate ions mimic substrate nucleotide phosphates.
RCSB
Y
RCSB
2002-06-06
REL
REL
SO4
SULFATE ION
HOH
water
SO4
601
2
SO4
SO4
601
A
SO4
602
2
SO4
SO4
602
A
SO4
603
2
SO4
SO4
603
A
SO4
604
2
SO4
SO4
604
A
WAT
1
3
HOH
HOH
605
A
WAT
2
3
HOH
HOH
606
A
WAT
3
3
HOH
HOH
607
A
WAT
4
3
HOH
HOH
608
A
WAT
5
3
HOH
HOH
609
A
WAT
6
3
HOH
HOH
610
A
WAT
7
3
HOH
HOH
611
A
WAT
8
3
HOH
HOH
612
A
WAT
9
3
HOH
HOH
613
A
WAT
10
3
HOH
HOH
614
A
WAT
11
3
HOH
HOH
615
A
WAT
12
3
HOH
HOH
616
A
WAT
13
3
HOH
HOH
617
A
WAT
14
3
HOH
HOH
618
A
WAT
15
3
HOH
HOH
619
A
WAT
16
3
HOH
HOH
620
A
WAT
17
3
HOH
HOH
621
A
WAT
18
3
HOH
HOH
622
A
WAT
19
3
HOH
HOH
623
A
WAT
20
3
HOH
HOH
624
A
WAT
21
3
HOH
HOH
625
A
WAT
22
3
HOH
HOH
626
A
WAT
23
3
HOH
HOH
627
A
WAT
24
3
HOH
HOH
628
A
WAT
25
3
HOH
HOH
629
A
WAT
26
3
HOH
HOH
630
A
WAT
27
3
HOH
HOH
631
A
WAT
28
3
HOH
HOH
632
A
WAT
29
3
HOH
HOH
633
A
WAT
30
3
HOH
HOH
634
A
WAT
31
3
HOH
HOH
635
A
WAT
32
3
HOH
HOH
636
A
WAT
33
3
HOH
HOH
637
A
WAT
34
3
HOH
HOH
638
A
WAT
35
3
HOH
HOH
639
A
WAT
36
3
HOH
HOH
640
A
WAT
37
3
HOH
HOH
641
A
WAT
38
3
HOH
HOH
642
A
WAT
39
3
HOH
HOH
643
A
WAT
40
3
HOH
HOH
644
A
WAT
41
3
HOH
HOH
645
A
WAT
42
3
HOH
HOH
646
A
WAT
43
3
HOH
HOH
647
A
WAT
44
3
HOH
HOH
648
A
WAT
45
3
HOH
HOH
649
A
WAT
46
3
HOH
HOH
650
A
WAT
47
3
HOH
HOH
651
A
WAT
48
3
HOH
HOH
652
A
WAT
49
3
HOH
HOH
653
A
WAT
50
3
HOH
HOH
654
A
WAT
51
3
HOH
HOH
655
A
WAT
52
3
HOH
HOH
656
A
WAT
53
3
HOH
HOH
657
A
WAT
54
3
HOH
HOH
658
A
WAT
55
3
HOH
HOH
659
A
WAT
56
3
HOH
HOH
660
A
WAT
57
3
HOH
HOH
661
A
WAT
58
3
HOH
HOH
662
A
WAT
59
3
HOH
HOH
663
A
WAT
60
3
HOH
HOH
664
A
WAT
61
3
HOH
HOH
665
A
WAT
62
3
HOH
HOH
666
A
WAT
63
3
HOH
HOH
667
A
WAT
64
3
HOH
HOH
668
A
WAT
65
3
HOH
HOH
669
A
WAT
66
3
HOH
HOH
670
A
WAT
67
3
HOH
HOH
671
A
WAT
68
3
HOH
HOH
672
A
WAT
69
3
HOH
HOH
673
A
WAT
70
3
HOH
HOH
674
A
WAT
71
3
HOH
HOH
675
A
WAT
72
3
HOH
HOH
676
A
WAT
73
3
HOH
HOH
677
A
WAT
74
3
HOH
HOH
678
A
WAT
75
3
HOH
HOH
679
A
WAT
76
3
HOH
HOH
680
A
WAT
77
3
HOH
HOH
681
A
WAT
78
3
HOH
HOH
682
A
WAT
79
3
HOH
HOH
683
A
WAT
80
3
HOH
HOH
684
A
WAT
81
3
HOH
HOH
685
A
WAT
82
3
HOH
HOH
686
A
WAT
83
3
HOH
HOH
687
A
WAT
84
3
HOH
HOH
688
A
WAT
85
3
HOH
HOH
689
A
WAT
86
3
HOH
HOH
690
A
WAT
87
3
HOH
HOH
691
A
WAT
88
3
HOH
HOH
692
A
WAT
89
3
HOH
HOH
693
A
WAT
90
3
HOH
HOH
694
A
WAT
91
3
HOH
HOH
695
A
WAT
92
3
HOH
HOH
696
A
WAT
93
3
HOH
HOH
697
A
WAT
94
3
HOH
HOH
698
A
WAT
95
3
HOH
HOH
699
A
WAT
96
3
HOH
HOH
700
A
WAT
97
3
HOH
HOH
701
A
WAT
98
3
HOH
HOH
702
A
WAT
99
3
HOH
HOH
703
A
WAT
100
3
HOH
HOH
704
A
WAT
101
3
HOH
HOH
705
A
WAT
102
3
HOH
HOH
706
A
WAT
103
3
HOH
HOH
707
A
WAT
104
3
HOH
HOH
708
A
WAT
105
3
HOH
HOH
709
A
WAT
106
3
HOH
HOH
710
A
WAT
107
3
HOH
HOH
711
A
WAT
108
3
HOH
HOH
712
A
WAT
109
3
HOH
HOH
713
A
WAT
110
3
HOH
HOH
714
A
WAT
111
3
HOH
HOH
715
A
WAT
112
3
HOH
HOH
716
A
WAT
113
3
HOH
HOH
717
A
WAT
114
3
HOH
HOH
718
A
WAT
115
3
HOH
HOH
719
A
WAT
116
3
HOH
HOH
720
A
WAT
117
3
HOH
HOH
721
A
WAT
118
3
HOH
HOH
722
A
WAT
119
3
HOH
HOH
723
A
WAT
120
3
HOH
HOH
724
A
WAT
121
3
HOH
HOH
725
A
WAT
122
3
HOH
HOH
726
A
WAT
123
3
HOH
HOH
727
A
WAT
124
3
HOH
HOH
728
A
WAT
125
3
HOH
HOH
729
A
WAT
126
3
HOH
HOH
730
A
WAT
127
3
HOH
HOH
731
A
WAT
128
3
HOH
HOH
732
A
WAT
129
3
HOH
HOH
733
A
WAT
130
3
HOH
HOH
734
A
WAT
131
3
HOH
HOH
735
A
WAT
132
3
HOH
HOH
736
A
WAT
133
3
HOH
HOH
737
A
WAT
134
3
HOH
HOH
738
A
WAT
135
3
HOH
HOH
739
A
WAT
136
3
HOH
HOH
740
A
WAT
137
3
HOH
HOH
741
A
WAT
138
3
HOH
HOH
742
A
WAT
139
3
HOH
HOH
743
A
WAT
140
3
HOH
HOH
744
A
WAT
141
3
HOH
HOH
745
A
WAT
142
3
HOH
HOH
746
A
MET
1
n
1
MET
1
A
LYS
2
n
2
LYS
2
A
LYS
3
n
3
LYS
3
A
ILE
4
n
4
ILE
4
A
ILE
5
n
5
ILE
5
A
LEU
6
n
6
LEU
6
A
THR
7
n
7
THR
7
A
ILE
8
n
8
ILE
8
A
GLY
9
n
9
GLY
9
A
CYS
10
n
10
CYS
10
A
PRO
11
n
11
PRO
11
A
GLY
12
n
12
GLY
12
A
SER
13
n
13
SER
13
A
GLY
14
n
14
GLY
14
A
LYS
15
n
15
LYS
15
A
SER
16
n
16
SER
16
A
THR
17
n
17
THR
17
A
TRP
18
n
18
TRP
18
A
ALA
19
n
19
ALA
19
A
ARG
20
n
20
ARG
20
A
GLU
21
n
21
GLU
21
A
PHE
22
n
22
PHE
22
A
ILE
23
n
23
ILE
23
A
ALA
24
n
24
ALA
24
A
LYS
25
n
25
LYS
25
A
ASN
26
n
26
ASN
26
A
PRO
27
n
27
PRO
27
A
GLY
28
n
28
GLY
28
A
PHE
29
n
29
PHE
29
A
TYR
30
n
30
TYR
30
A
ASN
31
n
31
ASN
31
A
ILE
32
n
32
ILE
32
A
ASN
33
n
33
ASN
33
A
ARG
34
n
34
ARG
34
A
ASP
35
n
35
ASP
35
A
ASP
36
n
36
ASP
36
A
TYR
37
n
37
TYR
37
A
ARG
38
n
38
ARG
38
A
GLN
39
n
39
GLN
39
A
SER
40
n
40
SER
40
A
ILE
41
n
41
ILE
41
A
MET
42
n
42
MET
42
A
ALA
43
n
43
ALA
43
A
HIS
44
n
44
HIS
44
A
GLU
45
n
45
GLU
45
A
GLU
46
n
46
GLU
46
A
ARG
47
n
47
ARG
47
A
ASP
48
n
48
ASP
48
A
GLU
49
n
49
GLU
49
A
TYR
50
n
50
TYR
50
A
LYS
51
n
51
LYS
51
A
TYR
52
n
52
TYR
52
A
THR
53
n
53
THR
53
A
LYS
54
n
54
LYS
54
A
LYS
55
n
55
LYS
55
A
LYS
56
n
56
LYS
56
A
GLU
57
n
57
GLU
57
A
GLY
58
n
58
GLY
58
A
ILE
59
n
59
ILE
59
A
VAL
60
n
60
VAL
60
A
THR
61
n
61
THR
61
A
GLY
62
n
62
GLY
62
A
MET
63
n
63
MET
63
A
GLN
64
n
64
GLN
64
A
PHE
65
n
65
PHE
65
A
ASP
66
n
66
ASP
66
A
THR
67
n
67
THR
67
A
ALA
68
n
68
ALA
68
A
LYS
69
n
69
LYS
69
A
SER
70
n
70
SER
70
A
ILE
71
n
71
ILE
71
A
LEU
72
n
72
LEU
72
A
TYR
73
n
73
TYR
73
A
GLY
74
n
74
GLY
74
A
GLY
75
n
75
GLY
75
A
ASP
76
n
76
ASP
76
A
SER
77
n
77
SER
77
A
VAL
78
n
78
VAL
78
A
LYS
79
n
79
LYS
79
A
GLY
80
n
80
GLY
80
A
VAL
81
n
81
VAL
81
A
ILE
82
n
82
ILE
82
A
ILE
83
n
83
ILE
83
A
SER
84
n
84
SER
84
A
ASP
85
n
85
ASP
85
A
THR
86
n
86
THR
86
A
ASN
87
n
87
ASN
87
A
LEU
88
n
88
LEU
88
A
ASN
89
n
89
ASN
89
A
PRO
90
n
90
PRO
90
A
GLU
91
n
91
GLU
91
A
ARG
92
n
92
ARG
92
A
ARG
93
n
93
ARG
93
A
LEU
94
n
94
LEU
94
A
ALA
95
n
95
ALA
95
A
TRP
96
n
96
TRP
96
A
GLU
97
n
97
GLU
97
A
THR
98
n
98
THR
98
A
PHE
99
n
99
PHE
99
A
ALA
100
n
100
ALA
100
A
LYS
101
n
101
LYS
101
A
GLU
102
n
102
GLU
102
A
TYR
103
n
103
TYR
103
A
GLY
104
n
104
GLY
104
A
TRP
105
n
105
TRP
105
A
LYS
106
n
106
LYS
106
A
VAL
107
n
107
VAL
107
A
GLU
108
n
108
GLU
108
A
HIS
109
n
109
HIS
109
A
LYS
110
n
110
LYS
110
A
VAL
111
n
111
VAL
111
A
PHE
112
n
112
PHE
112
A
ASP
113
n
113
ASP
113
A
VAL
114
n
114
VAL
114
A
PRO
115
n
115
PRO
115
A
TRP
116
n
116
TRP
116
A
THR
117
n
117
THR
117
A
GLU
118
n
118
GLU
118
A
LEU
119
n
119
LEU
119
A
VAL
120
n
120
VAL
120
A
LYS
121
n
121
LYS
121
A
ARG
122
n
122
ARG
122
A
ASN
123
n
123
ASN
123
A
SER
124
n
124
SER
124
A
LYS
125
n
125
LYS
125
A
ARG
126
n
126
ARG
126
A
GLY
127
n
127
GLY
127
A
THR
128
n
128
THR
128
A
LYS
129
n
129
LYS
129
A
ALA
130
n
130
ALA
130
A
VAL
131
n
131
VAL
131
A
PRO
132
n
132
PRO
132
A
ILE
133
n
133
ILE
133
A
ASP
134
n
134
ASP
134
A
VAL
135
n
135
VAL
135
A
LEU
136
n
136
LEU
136
A
ARG
137
n
137
ARG
137
A
SER
138
n
138
SER
138
A
MET
139
n
139
MET
139
A
TYR
140
n
140
TYR
140
A
LYS
141
n
141
LYS
141
A
SER
142
n
142
SER
142
A
MET
143
n
143
MET
143
A
ARG
144
n
144
ARG
144
A
GLU
145
n
145
GLU
145
A
TYR
146
n
146
TYR
146
A
LEU
147
n
147
LEU
147
A
GLY
148
n
148
GLY
148
A
LEU
149
n
149
LEU
149
A
PRO
150
n
150
PRO
150
A
VAL
151
n
151
VAL
151
A
TYR
152
n
152
TYR
152
A
n
153
153
A
n
154
154
A
n
155
155
A
n
156
156
A
n
157
157
A
n
158
158
A
n
159
159
A
n
160
160
A
n
161
161
A
n
162
162
A
n
163
163
A
n
164
164
A
n
165
165
A
n
166
166
A
n
167
167
A
n
168
168
A
n
169
169
A
n
170
170
A
n
171
171
A
n
172
172
A
n
173
173
A
n
174
174
A
n
175
175
A
n
176
176
A
n
177
177
A
n
178
178
A
n
179
179
A
n
180
180
A
n
181
181
A
author_defined_assembly
2
dimeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_655
-x+1,y,-z+1/2
crystal symmetry operation
65.3000000000
0.0000000000
33.9500000000
A
N
TYR
30
A
N
TYR
30
A
O
ILE
82
A
O
ILE
82
A
O
ILE
83
A
O
ILE
83
A
N
ILE
5
A
N
ILE
5
A
N
ILE
4
A
N
ILE
4
A
O
LYS
106
A
O
LYS
106
1
A
ASN
153
A
ASN
153
1
Y
1
A
GLY
154
A
GLY
154
1
Y
1
A
THR
155
A
THR
155
1
Y
1
A
PRO
156
A
PRO
156
1
Y
1
A
GLY
157
A
GLY
157
1
Y
1
A
LYS
158
A
LYS
158
1
Y
1
A
PRO
159
A
PRO
159
1
Y
1
A
LYS
160
A
LYS
160
1
Y
1
A
ALA
161
A
ALA
161
1
Y
1
A
VAL
162
A
VAL
162
1
Y
1
A
ILE
163
A
ILE
163
1
Y
1
A
PHE
164
A
PHE
164
1
Y
1
A
ASP
165
A
ASP
165
1
Y
1
A
VAL
166
A
VAL
166
1
Y
1
A
ASP
167
A
ASP
167
1
Y
1
A
GLY
168
A
GLY
168
1
Y
1
A
THR
169
A
THR
169
1
Y
1
A
LEU
170
A
LEU
170
1
Y
1
A
ALA
171
A
ALA
171
1
Y
1
A
LYS
172
A
LYS
172
1
Y
1
A
MET
173
A
MET
173
1
Y
1
A
ASN
174
A
ASN
174
1
Y
1
A
GLY
175
A
GLY
175
1
Y
1
A
ARG
176
A
ARG
176
1
Y
1
A
GLY
177
A
GLY
177
1
Y
1
A
PRO
178
A
PRO
178
1
Y
1
A
TYR
179
A
TYR
179
1
Y
1
A
ASP
180
A
ASP
180
1
Y
1
A
LEU
181
A
LEU
181
1
Y
1
A
TYR
52
-68.09
81.74
1
A
SER
84
-70.20
40.64
1
A
PHE
112
-117.91
79.79
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
34.4
3.36
0.00
0.00
3.89
0.00
-7.26
0.2310000
0.009
0.2100000
2.00
19.01
655
14121
13119
5.0
92.9
RANDOM
1
RESTRAINED
THROUGHOUT
0.0
0.0
SIR
Engh & Huber
FLAT MODEL
52.5142
0.38958
0.27
0.22
2.00
19.01
142
1403
20
0
1241
0.006
1.0
20.4
0.66
0.97
1.50
1.64
2.00
1.29
2.00
2.00
2.50
0.2770000
0.029
0.2780000
2.13
90
1868
6
4.6
85.2
13.7
2.00
20.0
1LY1
14453
12892
0
0
0.0510000
1
15.3
89.2
0.2230000
2.00
2.06
4.3
77.7
phasing
SOLVE
refinement
CNS
0.9
data reduction
DENZO
data scaling
SCALEPACK
Structure and Mechanism of T4 Polynucleotide Kinase
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
A
GLY
14
A
GLY
14
HELX_P
A
ASN
26
A
ASN
26
1
1
13
A
ASN
33
A
ASN
33
HELX_P
A
MET
42
A
MET
42
1
2
10
A
GLU
46
A
GLU
46
HELX_P
A
TYR
50
A
TYR
50
5
3
5
A
THR
53
A
THR
53
HELX_P
A
TYR
73
A
TYR
73
1
4
21
A
ASN
89
A
ASN
89
HELX_P
A
GLY
104
A
GLY
104
1
5
16
A
PRO
115
A
PRO
115
HELX_P
A
SER
124
A
SER
124
1
6
10
A
LYS
125
A
LYS
125
HELX_P
A
ALA
130
A
ALA
130
5
7
6
A
PRO
132
A
PRO
132
HELX_P
A
GLY
148
A
GLY
148
1
8
17
TRANSFERASE
PNK, KINASE, PHOSPHATASE, POLYNUCLEOTIDE, T4, PHAGE, TRANSFERASE
KIPN_BPT4
UNP
1
1
P06855
MKKIILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSIMAHEERDEYKYTKKKEGIVTGMQFDTAKSILYGGDSVKG
VIISDTNLNPERRLAWETFAKEYGWKVEHKVFDVPWTELVKRNSKRGTKAVPIDVLRSMYKSMREYLGLPVYNGTPGKPK
AVIFDVDGTLAKMNGRGPYDL
1
181
1LY1
1
181
P06855
A
1
1
181
4
parallel
parallel
parallel
A
PHE
29
A
PHE
29
A
ILE
32
A
ILE
32
A
GLY
80
A
GLY
80
A
ILE
83
A
ILE
83
A
LYS
3
A
LYS
3
A
ILE
8
A
ILE
8
A
LYS
106
A
LYS
106
A
VAL
111
A
VAL
111
BINDING SITE FOR RESIDUE SO4 A 601
A
SO4
601
Software
10
BINDING SITE FOR RESIDUE SO4 A 602
A
SO4
602
Software
6
BINDING SITE FOR RESIDUE SO4 A 603
A
SO4
603
Software
2
BINDING SITE FOR RESIDUE SO4 A 604
A
SO4
604
Software
3
A
CYS
10
A
CYS
10
10
1_555
A
PRO
11
A
PRO
11
10
1_555
A
GLY
12
A
GLY
12
10
1_555
A
SER
13
A
SER
13
10
1_555
A
GLY
14
A
GLY
14
10
1_555
A
LYS
15
A
LYS
15
10
1_555
A
SER
16
A
SER
16
10
1_555
A
ARG
126
A
ARG
126
10
1_555
A
HOH
623
F
HOH
10
1_555
A
HOH
658
F
HOH
10
1_555
A
ARG
34
A
ARG
34
6
1_555
A
ARG
38
A
ARG
38
6
1_555
A
ASP
85
A
ASP
85
6
1_555
A
THR
86
A
THR
86
6
1_555
A
HOH
608
F
HOH
6
1_555
A
HOH
609
F
HOH
6
1_555
A
GLU
108
A
GLU
108
2
1_555
A
HIS
109
A
HIS
109
2
1_555
A
ARG
93
A
ARG
93
3
1_555
A
GLU
97
A
GLU
97
3
1_555
A
HIS
109
A
HIS
109
3
1_555
20
C 2 2 21